bot

app.py

@@ -1,11 +1,7 @@
 import gradio as gr
 import json
 from rag.rag_pipeline import RAGPipeline
-from utils.prompts import highlight_prompt, evidence_based_prompt
-from utils.prompts import (
-    sample_questions,
-)
-
+from utils.prompts import highlight_prompt, evidence_based_prompt, sample_questions
 from config import STUDY_FILES
 
 # Cache for RAG pipelines
@@ -22,7 +18,7 @@ def get_rag_pipeline(study_name):
     return rag_cache[study_name]
 
 
-def query_rag(study_name: str, question: str, prompt_type: str) -> str:
+def chat_function(message, history, study_name, prompt_type):
     rag = get_rag_pipeline(study_name)
 
     if prompt_type == "Highlight":
@@ -32,9 +28,7 @@ def query_rag(study_name: str, question: str, prompt_type: str) -> str:
     else:
         prompt = None
 
-    # Use the prepared context in the query
-    response = rag.query(question, prompt_template=prompt)
-
+    response = rag.query(message, prompt_template=prompt)
     return response.response
 
 
@@ -48,55 +42,48 @@ def get_study_info(study_name):
         return "Invalid study name"
 
 
-def update_sample_questions(study_name):
-    return gr.Dropdown(choices=sample_questions.get(study_name, []), interactive=True)
-
-
 with gr.Blocks() as demo:
     gr.Markdown("# RAG Pipeline Demo")
 
     with gr.Row():
         study_dropdown = gr.Dropdown(
-            choices=list(STUDY_FILES.keys()), label="Select Study"
-        )
-        study_info = gr.Markdown(label="Study Information")
-
-    study_dropdown.change(get_study_info, inputs=[study_dropdown], outputs=[study_info])
-
-    with gr.Row():
-        question_input = gr.Textbox(label="Enter your question")
-        sample_question_dropdown = gr.Dropdown(
-            choices=[], label="Sample Questions", interactive=True
+            choices=list(STUDY_FILES.keys()),
+            label="Select Study",
+            value=list(STUDY_FILES.keys())[0],
         )
-
-    study_dropdown.change(
-        update_sample_questions,
-        inputs=[study_dropdown],
-        outputs=[sample_question_dropdown],
-    )
-    sample_question_dropdown.change(
-        lambda x: x, inputs=[sample_question_dropdown], outputs=[question_input]
-    )
+        study_info = gr.Markdown()
 
     prompt_type = gr.Radio(
-        [
-            "Default",
-            "Highlight",
-            "Evidence-based",
-        ],
+        ["Default", "Highlight", "Evidence-based"],
         label="Prompt Type",
         value="Default",
     )
 
-    submit_button = gr.Button("Submit")
+    chatbot = gr.Chatbot()
+    msg = gr.Textbox()
+    clear = gr.Button("Clear")
 
-    answer_output = gr.Markdown(label="Answer")
+    def user(user_message, history):
+        return "", history + [[user_message, None]]
 
-    submit_button.click(
-        query_rag,
-        inputs=[study_dropdown, question_input, prompt_type],
-        outputs=[answer_output],
+    def bot(history, study_name, prompt_type):
+        user_message = history[-1][0]
+        bot_message = chat_function(user_message, history, study_name, prompt_type)
+        history[-1][1] = bot_message
+        return history
+
+    msg.submit(user, [msg, chatbot], [msg, chatbot], queue=False).then(
+        bot, [chatbot, study_dropdown, prompt_type], chatbot
     )
+    clear.click(lambda: None, None, chatbot, queue=False)
+
+    study_dropdown.change(
+        fn=get_study_info,
+        inputs=study_dropdown,
+        outputs=study_info,
+    ).then(lambda: None, None, chatbot, queue=False)
+
+    gr.Examples(examples=sample_questions[list(STUDY_FILES.keys())[0]], inputs=msg)
 
 if __name__ == "__main__":
     demo.launch(share=True, debug=True)

utils/prompts.py

@@ -73,16 +73,6 @@ vaccine_coverage_prompt = PromptTemplate(
 sample_questions = {
     "Vaccine Coverage": [
         "What are the vaccine coverage rates reported in the study?",
-        "What proportion of vaccines were administered within the recommended age range?",
-        "What is the immunisation uptake reported in the study?",
-        "What are the vaccine drop-out rates mentioned in the document?",
-        "What are the intentions to vaccinate reported in the study?",
-        "How is vaccine confidence described in the document?",
-        "What factors influencing vaccine hesitancy are identified in the study?",
-        "Are there any demographic differences in vaccine coverage or uptake?",
-        "What interventions, if any, were implemented to improve vaccine coverage?",
-        "How does the study address equity in vaccine distribution and access?",
-        "What is the geographical scope of the study (e.g., urban, rural, national)?",
         "Are there any reported adverse events following immunization (AEFI)?",
         "How does the study account for different vaccine types or schedules?",
         "Extract and present in a tabular format the following variables for each vaccine coverage study: STUDYID, AUTHOR, YEAR, TITLE, PUBLICATION_TYPE, STUDY_DESIGN, STUDY_AREA_REGION, STUDY_POPULATION, IMMUNISABLE_DISEASE_UNDER_STUDY, ROUTE_OF_VACCINE_ADMINISTRATION, DURATION_OF_STUDY, DURATION_IN_RELATION_TO_COVID19, VACCINE_COVERAGE_RATES, PROPORTION_ADMINISTERED_WITHIN_RECOMMENDED_AGE, IMMUNISATION_UPTAKE, VACCINE_DROP_OUT_RATES, INTENTIONS_TO_VACCINATE, VACCINE_CONFIDENCE, HESITANCY_FACTORS, DEMOGRAPHIC_DIFFERENCES, INTERVENTIONS, EQUITY_CONSIDERATIONS, GEOGRAPHICAL_SCOPE, AEFI, VACCINE_TYPES, and STUDY_COMMENTS.",
@@ -90,16 +80,6 @@ sample_questions = {
     "Ebola Virus": [
         "What is the sample size of the study?",
         "What is the type of plasma used in the study?",
-        "What is the dosage and frequency of administration of the plasma?",
-        "Are there any reported side effects?",
-        "What is the change in viral load after treatment?",
-        "How many survivors were there in the intervention group compared to the control group?",
-        "What was the study design (e.g., RCT, observational)?",
-        "What were the inclusion and exclusion criteria for participants?",
-        "Were there any subgroup analyses performed?",
-        "What was the duration of follow-up?",
-        "Were there any reported long-term outcomes or sequelae?",
-        "How was the severity of Ebola virus disease assessed?",
         "What biosafety measures were implemented during the study?",
         "Were there any ethical considerations or challenges reported?",
         "Create a structured table for each Ebola virus study, including the following information: STUDYID, AUTHOR, YEAR, TITLE, PUBLICATION_TYPE, STUDY_DESIGN, STUDY_AREA_REGION, STUDY_POPULATION, SAMPLE_SIZE, PLASMA_TYPE, DOSAGE, FREQUENCY, SIDE_EFFECTS, VIRAL_LOAD_CHANGE, SURVIVAL_RATE, INCLUSION_CRITERIA, EXCLUSION_CRITERIA, SUBGROUP_ANALYSES, FOLLOW_UP_DURATION, LONG_TERM_OUTCOMES, DISEASE_SEVERITY_ASSESSMENT, BIOSAFETY_MEASURES, ETHICAL_CONSIDERATIONS, and STUDY_COMMENTS.",
@@ -108,17 +88,6 @@ sample_questions = {
         "What is the main objective of the study?",
         "What is the study design?",
         "What disease condition is being studied?",
-        "What are the main outcome measures in the study?",
-        "What is the sensitivity and specificity of the Gene Xpert test?",
-        "How does the cost of the Gene Xpert testing strategy compare to other methods?",
-        "What is the turnaround time for Gene Xpert results compared to conventional methods?",
-        "Are there any reported challenges in implementing Gene Xpert in the study setting?",
-        "How does Gene Xpert performance vary across different sample types or patient populations?",
-        "What quality control measures were implemented in the study?",
-        "Were there any reported equipment failures or technical issues?",
-        "How does the study address the impact of Gene Xpert on patient outcomes or clinical decision-making?",
-        "What training or human resource requirements were reported for Gene Xpert implementation?",
-        "How does the study consider the scalability and sustainability of Gene Xpert use?",
         "Extract and present in a tabular format the following variables for each Gene Xpert study: STUDYID, AUTHOR, YEAR, TITLE, PUBLICATION_TYPE, STUDY_DESIGN, STUDY_AREA_REGION, STUDY_POPULATION, DISEASE_CONDITION, OBJECTIVE, OUTCOME_MEASURES, SENSITIVITY, SPECIFICITY, COST_COMPARISON, TURNAROUND_TIME, IMPLEMENTATION_CHALLENGES, PERFORMANCE_VARIATIONS, QUALITY_CONTROL, EQUIPMENT_ISSUES, PATIENT_OUTCOME_IMPACT, TRAINING_REQUIREMENTS, SCALABILITY_CONSIDERATIONS, and STUDY_COMMENTS.",
     ],
 }